Workshop Description

This workshop provides an introduction to the microbiome analyses from the raw sequence data generated from the next-generation sequencing platforms. We will cover how to perform the 16S rRNA-based analysis using an open-source bioinformatics pipeline QIIME. We will also cover some downstream analyses of the microbiome data beyond QIIME, including statistical analyses and functional analyses.

We will demonstrate the 16S rRNA gene analysis using QIIME

  1. Run QIIME on Hoffman2 or local
  2. Sequence data preparation
  3. Operational Taxonomic Units (OTU) picking, Taxonomic assignment & inferring phylogeny

Slides for day 1 can be found here.

We will demonstrate the 16S rRNA gene analysis using QIIME

  1. Microbiome diversity analyses

Slides for day 2 can be found here.

On day 3 we will learn functional analyses of the microbiome

Slides for day 3 can be found here.

Workshop Materials

  • Attendees are required to have a Hoffman2 account. To apply for an account, click here. UCLA participants who lack a faculty sponsor and non-UCLA participants may apply for a temporary Hoffman2 account, requesting sponsorship from Collaboratory Workshops.
  • We strongly encourage attendees to bring a laptop capable of accessing UCLA’s WiFi.


Baochen Shi, Ph.D., is a postdoc working with Dr. Huiying Li in the department of Molecular and Medical Pharmacology. By studying genomes and transcriptomes of the microorganisms living inside and on the humans, he aims to understand how human microbiome play a role in health and disease. Prior to joining UCLA, he completed his Ph.D. in the bioinformatics lab of Prof. Runsheng Chen in the Institute of Biophysics, Chinese Academy of Sciences.



I learned a lot and was surprised that there were slides that were useful that extended analyses to other areas of metagenomics. Baochen was really patient and helpful.
Spring 2017 Student

I’m glad that you actually have to change some file names from the slides so people actually try to understand what the slides mean– that they are examples but you can’t just mindlessly copy and paste.

Spring 2017 Student

I also liked how Shin addressed things related to publications and really developed students questions.

Spring 2017 Student

Workshop Details

Prerequisites: None
Length: 3 days, 2 hrs per day
Level: Introductory
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 10

Fall 2019 Dates